[BioC] limma question

[James W. MacDonald]

Sun, Yezhou wrote:
> Hi, Jim,
> 
> I tried what you suggested but it's still not working. Got same error
> message:
> 
> 
>>fit<-lmFit(d[, -1], design)
> 
> Error in qr(x) : NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> NAs introduced by coercion 
> 
> 
> I think the problem is still in data frame but I don't know what it is.
> The user guide has no detailed description for single channel data set. 

Affy data are single channel, and I think there are two or three 
examples in the user guide.

lmFit() is expecting some sort of BioC type object (exprSet, MAlist, 
marrayNorm, PLMset) or a numeric matrix. A matrix can only contain data 
of one type (character, factor, numeric, etc), whereas a data.frame can 
contain data of mixed types. One of the first things lmFit() is doing to 
your data.frame is coercing to a matrix, which I think is the reason for 
the Warning message saying NAs introduced by coercion. I figured that 
the first column was the problem, but you need to see if there are any 
other NAs in the data.frame, or better yet do

new.d <- as.matrix(d[,-1])

and look for the NAs.

Best,

Jim


-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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